regarding different names of the fields in BASE1 and BASE2, but there was
another post about that.
Best Regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinformatic
if(ch(2) > 100)
2:ch(2)
else
2:100
}
else
filter out the spot.
Best Regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinformatics user
t2\toption2 0
> >
> > Alternatively BASE2 could handle an empty field an insert the proper
> value.
> >
> > Hope I saved someone some hours figuring this out.
> >
> > I stil
igure eclipse with tomcat so I
could set breakpoints and inspect the variables in runtime. I saw in another
post that you in Lund did not do this, but for people not very familiar with
the code I think this is a huge benefit, at least for saving time. I
recommend it, but I spent some time to set eclipse up.
paste job each time base1
was updated and I had to re-update my custom files. I hope BASE2 can do this
in a more neat way.
Best Regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinformatics user support (
mes in my base1 plug-in, and I would still not know the
field name to translate from. I looked a round a bit and found that
something at least had happened to 'position' from the last version.
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-R
t be extended should use the protected
or public modifier. But there might be other downsides with that approach
that I don't see.
Best Regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinforma
on of ch(1) and ch(2) in BASE2? How do I now
that my ratio is A/B and not B/A? I also searched for this information in
the API.
Best regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinformatics user supp
Hi. I also think that Nicklas' "Abstract" approach will work well for me. I
just need to refresh my java skills and test it out to be sure. I will get
back with some detailed proposals in a few days.
Vegard.
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:basedb-devel-
> [EMAIL PR
ve any rights in the subversion to upload my code so I provide my
files here:
http://insilico.titan.uio.no/~vegardny/base2/VegardsBase1PluginExecuterModif
ication.zip
Hope you make it fit in.
Best regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospi
he bug to
you.
Also I found another bug/feature: the "leaveStdin"/"leaveStdout"-flags did
not seem to have any effect. The files were stored anyway. For my part this
is ok.
Best regards
Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radium
Hi. I have a proposal.
>Are there other item types that may need files?
>http://base.thep.lu.se/ticket/721. ..
I have sometimes heard the need to store quality control reports for
extracts and labeled extracts. A lab tool called BioAnalyzer makes a file
with a plot to better assess the quality (
I have some jobs I want to delete, but I am not allowed to. I think the
reason is that they are still in "Executing" mode, according to the job
list.
In reality they are not executing, this is just old trial and error runs of
plug-ins that apparently failed in unexpected ways. I can't find a wa
> 15 nov 2007 kl. 21.32 Bob MacCallum wrote:
>
> > Vegard, did you come up with a work-around? Should one import all
> > data "straight" and use the dyes as a proxy for the channel number?
No I did not. I planned to either convince my self that BASE2's model was
sufficient or make a dye-swa
I think that uploading files using BASE2's http-upload can become cumbersome
and prone to errors with bigger/many files. We hope to produce a lot of data
in the near future and this might be a problem.
I have an idea of a "Import server side files"-plug-in. This will work in
this way:
1. You upl
I have some ideas, though you might already have tried them.
1. Removing all Tab2MageImporter.jar files, new and old. Delete
tomcat/work. Restart tomcat. Edit and save the plugin definition without
changing anything. Now (or earlier) you should get a red box saying that
BASE2 does not find
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